SAXSdb — 9vvr

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1. Structure Basics

entry_id	9vvr
deposition_date	2025-07-16
title	Structure of the bacteriophage E1004 tail
keywords	Complex, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	73.99 Å
rg_electron	73.20 Å
i0	15277600000.00
molecular_weight	1034100.0 kDa
excluded_volume	1286000 Å³
envelope_volume	2127600 Å³
shell_volume	228920 Å³
envelope_diameter	234.9 Å
shell_rg	80.97 Å
envelope_rg	72.31 Å
shape_rg	73.17 Å
total_rg	73.39 Å
total_atoms	72911
n_residues	9294
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	272.9 Å
rg_real	77.27 Å
rg_real_error	1.77 Å
i0_real	1.5310e+10
i0_real_error	3.2600e+08
rg_reciprocal	74.84 Å
i0_reciprocal	15310000000.0000
total_estimate	0.8932
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	91.0 Å
skewness	0.508
kurtosis	0.363
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.9356
highest_alpha	1783000000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.702; Stabil: 0.885; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.935

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Tail spike protein
formula_weight	90533.8 kDa
src_method	nat
entity_count	18

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
atom_count	72911

MSTITQFPSGNTQYRIEFDYLARTFVVVTLVNSSNPTLNRVLEVGRDYRFLNPTMIEMLVDQSGFDIVRIHRQTGTDLVVDFRNGSVLTASDLTNSELQAIHIAEEGRDQTVDLAKEYADAAGSSAGNAKDSEDEARRIAESIREAGLIGYITRRSFEKGYNVTTWSEVLLWEEDGDYYRWDGTLPKNVPAGSTPETSGGIGLGAWVSVGDAALRSQISNPEGAILYPELQMARWRDEGDVRGWGAKGDGVTDSTENIAASLNSQKAVVASEGVFSSSGINSNYCNLDGRGSGVLSHRSSTGNYLVFNNPRTGRLSNITVESNKATDTTQGQQVSLAGGSDVTVSDVNFSNVKGTGFSLIAYPNDVPPDGLMIKGIRGSYSGYATNKAAGCVLADSSVNSLIDNVIAKNYPQFGAVELKGTASYNIVSNVIGTDCQHVTYNGTKGSIAPSNNLIKGVVANNPKYAAVVAGKGSTNLISDVLVDYSTSDARQAHGVTVEGSDNVINNVLMTGCDGTNSLGQAQTATITRFIDTANNNYASVFPSYSATGVITFESGSTRNFVEVKHPGRRNDLLSATGTISGADTIDGTDNSNVVHAPALGQYIGSMSGRFEWRIKSMSLPSGVLTSADKYRMLADGAVSLAVGGGTSSQVRLFTSDGTYRNISLTSGNVRLPTSSTGYLQLGSNAMTPDSTNTYALGSASRAWSGGFTQSAFTVVSDARDKTEPLNISDALLDAWSEVDFVQFQYLGRIEEKGADSARWHFGIIAQRAKEAFERHGIDAHRYGFLCFDSWDDVYEEDANGSRKLITPAGSRYGIRYEEVLILEAALMRRTIKRMQEALAVMSK

Entity 2 polymer

description	Nozzle protein
formula_weight	86595.6 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	S,V,X,Z,b,d

MPLITQSIKNLKGGISQQPDILRFSDQGESQVNCWSSESDGLQKRPPTVFKRRLNIDVESNPKFHLINRDEHEQYYIVFNGSNIQVVDLSGNQYSVSGAVEYVTSSNPRDDIRVVTVADYTFVVNRKVVVKGGSEKSHPGYNRKARALINLRGGQYGRTLKVGINGGVKVSHKLPAGNDAENDPPKVDAQAIGAAMRDLLVQAYPDFTFDLGSGFLLITAPSGTDINSVETEDGYANQLISPVLDTVQTISKLPLAAPNGYIIKIQGETNSSADEYYVMYDSNTKTWKETVEPGVITGFDVTTMPHALIRQSDGSFEFKTLDWSKRGSGNDDTNPMPSFVDATINDVFFYRNRLGFLSGENVIMSRSASYFAFFPKSVATLSDADPIDVAVSHPRISILKYAVPFSEQLLLWSDEVQFVMTSSGVLTSKSIQLDVGSEFALGDTARPFAVGRSVFFSAPRGSFTSIKRYFAVADVSDVKDADDTTGHVLSYIPNGVFDIQGTGTENYICVNSTGAYNRIYIYKFLFKDGVQLQASWSHWEFPKDDKILASASIGSTMFIVRQHQGGVDIEHLKFIKEATDFPSEPYRLHIDSKVSMVIPIGSYNADTYKTTVDIGAAYGGNAPSPGRYYLIDSQGAYVDLGDLTSISTVITLNGDWSGRTVFIGRPYLMSYKFSRFLIKIEDDSGTQSEDTGRLQLRRAWVNYKDTGALRLIVRNGEREFVNTFNGYTLGQQTIGTTNIGDGQYRFAMNGNALTTSLTLESNYPTPVSIVGCGWEASYAKKARSV

Entity 3 polymer

description	Adaptor protein
formula_weight	21457.0 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	T,U,W,Y,a,c,e,f,g,h,i,j

MAQYIPLNANDDLDAINDMLAAIGEPAVLQLDEGNADVSNAQRILHRVNRQVQAKGWNFNINEAAVLTPDVQDNRIRFLPSYLRVMTAGATSYYSNMGGYLYDLSTQSTTFTDPITVELVEMKPFSEMPVVFRDYIVTKASREFNAKFFGSPESELYLREQEAELYQQVMEYEMDTGRYNMMSDIGRD

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.110 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.11 Å
resolution_method	—
num_particles	50105

fit	/app/data/saxs_computation/vv/9vvr/9vvr.fit
pddf	/app/data/pr_computation/vv/9vvr/9vvr.pr.out
profile	/app/data/saxs_computation/vv/9vvr/9vvr.dat

Structure of the bacteriophage E1004 tail

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)